CIS peptide bond fixer too aggresive

Started by AsDawnBreaks

AsDawnBreaks Lv 1

I click on the button to fix, and it doesn't just tweak the area a bit, it swings my whole protein around. Rebuild works better to fix these now, as it only moves the area by a small amount. See screenshots (fixing just one issue).

brow42 Lv 1

I would suggest making a cut at the next u-turn or proline or glycine, probably downstream (but maybe upstream?). The 180 degree twist has to go somewhere.

AsDawnBreaks Lv 1

Just for fun, thought I'd mention using the new tool to fix all gave me a nearly straight protein. Rebuild works fine as an alternative.

Deleted user

This new CIS "fix" tool doesn't seem to be good for anything, just flips half the protein somewhere off to never-never land.

karstenw Lv 1

i band key locations or run zlb, and freeze my structures, then when it swings out just shake wiggle to restore protein.

brow42 Lv 1

Indeed, at least now you know it's there…rebuild will eventually eliminate these (by creating a twist) if you don't want Foldit to fix it for you. Before you'd never know they were there unless you were really really skilled at atom view (itskimo was godly at that).

I made a banding script to encourage creation/elimination of these bonds, but rebuild rejects so many poses when atoms are banded that I abandoned that approach.

jflat06 Staff Lv 1

Any time you change a backbone degree of freedom, it necessarily moves every residue down the chain. We get around this with a lot of the Foldit tools by inserting cuts and then resolving them behind the scenes. We already have tools for doing this, such as rebuild (as other people have mentioned).

This tool was introduced as a means to fix the problem directly, while letting the player deal with the side effects. The tool can't really be aggressive - there are 2 values for the omega angle in a peptide bond. Cis and trans. There is not in-between.

Brow's suggestion of inserting a cut somewhere down the chain is a good strategy for mitigating the side effects of the tool.

AsDawnBreaks Lv 1

Ok, I see. But could we have something that changes just enough to resolve it, not make it the opposite? Or even just make it an indicator you can turn on and off (like clash). It does not good to use if the protein is destroyed.